Reorders and some reindentation

packages/CLPBN/clpbn.yap

@@ -1,38 +1,34 @@
 
-:- module(clpbn, [{}/1,
+:- module(clpbn,
+	      [{}/1,
 	       clpbn_flag/2,
 	       set_clpbn_flag/2,
 	       clpbn_flag/3,
 	       clpbn_key/2,
+	       clpbn_init_graph/1,		  
 	       clpbn_init_solver/4,
 	       clpbn_run_solver/3,
+	       clpbn_finalize_solver/1,		  
 	       pfl_init_solver/5,
 	       pfl_run_solver/3,
-		  clpbn_finalize_solver/1,
-		  clpbn_init_graph/1,
 	       probability/2,
 	       conditional_probability/3,
 	       use_parfactors/1,
-		  op( 500, xfy, with)]).
+	       op(500, xfy, with)
+	      ]).
 	      
 :- use_module(library(atts)).
+
 :- use_module(library(bhash)).
+
 :- use_module(library(lists)).
+
 :- use_module(library(terms)).
+
 :- use_module(library(maplist)).
 
-%
-% avoid the overhead of using goal_expansion/2.
-%
-:- multifile
-	user:term_expansion/2.
-
-:- dynamic
-	user:term_expansion/2.
-
 :- attribute key/1, dist/2, evidence/1.
 
-
 :- use_module('clpbn/ve',
 	      [ve/3,
 	       check_if_ve_done/1,
@@ -43,6 +39,39 @@
 	       call_ve_ground_solver/6
 	      ]).
 
+:- use_module('clpbn/jt',
+	      [jt/3,
+	       init_jt_solver/4,
+	       run_jt_solver/3
+	      ]).
+
+:- use_module('clpbn/bdd',
+	      [bdd/3,
+	       init_bdd_solver/4,
+	       run_bdd_solver/3,
+	       init_bdd_ground_solver/5,
+	       run_bdd_ground_solver/3,
+	       call_bdd_ground_solver/6
+	      ]).
+
+:- use_module('clpbn/gibbs',
+	      [gibbs/3,
+	       check_if_gibbs_done/1,
+	       init_gibbs_solver/4,
+	       run_gibbs_solver/3
+	      ]).
+
+%% :- use_module('clpbn/bnt',
+%% 	      [do_bnt/3,
+%% 	       check_if_bnt_done/1
+%% 	      ]).
+
+:- use_module('clpbn/pgrammar',
+	      [init_pcg_solver/4,
+	       run_pcg_solver/3,
+	       pcg_init_graph/0
+	      ]).
+
 :- use_module('clpbn/horus_ground',
 	      [call_horus_ground_solver/6,
 	       check_if_horus_ground_solver_done/1,
@@ -59,47 +88,8 @@
 	       finalize_horus_lifted_solver/1
 	      ]).
 
-:- use_module('clpbn/jt',
-	      [jt/3,
-	       init_jt_solver/4,
-	       run_jt_solver/3
-	      ]).
-
-:- use_module('clpbn/bdd',
-	      [bdd/3,
-	       init_bdd_solver/4,
-	       run_bdd_solver/3,
-	       init_bdd_ground_solver/5,
-	       run_bdd_ground_solver/3,
-	       call_bdd_ground_solver/6
-	      ]).
-
-%% :- use_module('clpbn/bnt',
-%% 	      [do_bnt/3,
-%% 	       check_if_bnt_done/1
-%% 	      ]).
-
-:- use_module('clpbn/gibbs',
-	      [gibbs/3,
-	       check_if_gibbs_done/1,
-	       init_gibbs_solver/4,
-	       run_gibbs_solver/3
-	      ]).
-
-:- use_module('clpbn/pgrammar',
-	      [init_pcg_solver/4,
-	       run_pcg_solver/3,
-	       pcg_init_graph/0
-	      ]).
-
-:- use_module('clpbn/graphs',
-	      [
-	       clpbn2graph/1
-	      ]).
-
 :- use_module('clpbn/dists',
-	      [
+	      [dist/4,
-	       dist/4,
 	       get_dist/4,
 	       get_evidence_position/3,
 	       get_evidence_from_position/3,
@@ -107,33 +97,47 @@
 	      ]).
 
 :- use_module('clpbn/evidence',
-	      [
+	      [store_evidence/1,
-	       store_evidence/1,
 	       add_stored_evidence/2,
 	       incorporate_evidence/2,
 	       check_stored_evidence/2,
 	       put_evidence/2
 	      ]).
 	      
+:- use_module('clpbn/ground_factors',
+	      [generate_network/5]).
+
 :- use_module('clpbn/utils',
-	      [
+	      [sort_vars_by_key/3]).
-	       sort_vars_by_key/3
+
-	      ]).
+:- use_module('clpbn/graphs',
+	      [clpbn2graph/1]).
 
 :- use_module('clpbn/graphviz',
 	      [clpbn2gviz/4]).
 
-:- use_module(clpbn/ground_factors,
-	[generate_network/5]).
 
+%
+% avoid the overhead of using goal_expansion/2.
+%
+:- multifile user:term_expansion/2.
 
-:- dynamic solver/1,output/1,use/1,suppress_attribute_display/1, parameter_softening/1, em_solver/1, use_parfactors/1.
+:- dynamic user:term_expansion/2.
 
-solver(ve).
+:- dynamic
-em_solver(bp).
+	solver/1,
+	output/1,
+	use/1,
+	suppress_attribute_display/1,
+	parameter_softening/1,
+	em_solver/1,
+	use_parfactors/1.
 	
 :- meta_predicate probability(:,-), conditional_probability(:,:,-).
 
+
+solver(ve).
+em_solver(bp).
 %output(xbif(user_error)).
 %output(gviz(user_error)).
 output(no).
@@ -141,6 +145,7 @@ suppress_attribute_display(false).
 parameter_softening(m_estimate(10)).
 use_parfactors(off).
 
+
 clpbn_flag(Flag,Option) :-
 	clpbn_flag(Flag, Option, Option).
 
@@ -182,7 +187,7 @@ clpbn_flag(use_factors,Before,After) :-
 	dist(Dist, DistInfo, Key, Parents),
 	add_evidence(Var,Key,DistInfo,El)
 %	,writeln({Var = Key with Dist})
-.
+	.
 
 %
 % make sure a query variable is reachable by the garbage collector.
@@ -332,7 +337,6 @@ write_out(bdd, GVars, AVars, DiffVars) :-
 	bdd(GVars, AVars, DiffVars).
 write_out(bp, _GVars, _AVars, _DiffVars) :- 
 	writeln('interface not supported any longer').
-	%bp(GVars, AVars, DiffVars).
 write_out(gibbs, GVars, AVars, DiffVars) :-
 	gibbs(GVars, AVars, DiffVars).
 write_out(bnt, GVars, AVars, DiffVars) :-
@@ -530,6 +534,15 @@ user:term_expansion((A :- {}), ( :- true )) :-	 !, % evidence
 clpbn_key(Var,Key) :-
 	get_atts(Var, [key(Key)]).
 	
+	
+%
+% only useful for probabilistic context free grammars
+%
+clpbn_init_graph(pcg) :- !,
+	pcg_init_graph.
+clpbn_init_graph(_).
+
+
 %
 % This is a routine to start a solver, called by the learning procedures (ie, em).
 % LVs is a list of lists of variables one is interested in eventually marginalising out
@@ -544,14 +557,19 @@ clpbn_init_solver(LVs, Vs0, VarsWithUnboundKeys, State) :-
 
 clpbn_init_solver(gibbs, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_gibbs_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+	
 clpbn_init_solver(ve, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_ve_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+	
 clpbn_init_solver(bp, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_horus_ground_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+	
 clpbn_init_solver(jt, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_jt_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+	
 clpbn_init_solver(bdd, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_bdd_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+	
 clpbn_init_solver(pcg, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_pcg_solver(LVs, Vs0, VarsWithUnboundKeys, State).
 
@@ -560,7 +578,6 @@ clpbn_init_solver(pcg, LVs, Vs0, VarsWithUnboundKeys, State) :-
 % Vs is the full graph
 % Ps are the probabilities on LVs. 
 %
-%
 clpbn_run_solver(LVs, LPs, State) :-
 	solver(Solver),
 	clpbn_run_solver(Solver, LVs, LPs, State).
@@ -583,6 +600,13 @@ clpbn_run_solver(bdd, LVs, LPs, State) :-
 clpbn_run_solver(pcg, LVs, LPs, State) :-
 	run_pcg_solver(LVs, LPs, State).
 	
+clpbn_finalize_solver(State) :-
+	solver(bp), !,
+	functor(State, _, Last),
+	arg(Last, State, Info),
+	finalize_horus_ground_solver(Info).
+clpbn_finalize_solver(_State).
+
 
 %
 % This is a routine to start a solver, called by the learning procedures (ie, em).
@@ -637,19 +661,6 @@ pfl_run_solver(LVs, LPs, State, cbp) :- !,
 
 add_keys(Key1+V1,_Key2,Key1+V1).
 
-%
-% only useful for probabilistic context free grammars
-%
-clpbn_init_graph(pcg) :- !,
-	pcg_init_graph.
-clpbn_init_graph(_).
-
-clpbn_finalize_solver(State) :-
-	solver(bp), !,
-	functor(State, _, Last),
-	arg(Last, State, Info),
-	finalize_horus_ground_solver(Info).
-clpbn_finalize_solver(_State).
 
 probability(Goal, Prob) :-
 	findall(Prob, do_probability(Goal, [], Prob), [Prob]).

packages/CLPBN/clpbn/display.yap

@@ -12,6 +12,8 @@
 
 :- use_module(library(maplist)).
 
+:- use_module(library(atts)).
+
 :- attribute posterior/4.
 
 

packages/CLPBN/clpbn/ground_factors.yap

@@ -1,40 +1,34 @@
 
-%parfactor(
+:- module(pfl_ground_factors,
-%	[ability(P),grade(C,S), satisfaction(C,S,P)],
+	[generate_network/5,
-%        \phi = [....], 
-%       [P,C,S],
-%	[P \in [p1,p2,p4], C \in [c1,c3], S \in [s2,s3]]).
-%	[S \= s2])
-
-
-:- module(pfl_ground_factors, [
-          generate_network/5,
 	 f/3
 	]).
 
-:- use_module(library(bhash), [
+:- use_module(library(bhash),
-          b_hash_new/1,
+	[b_hash_new/1,
 	 b_hash_lookup/3,
 	 b_hash_insert/4,
-	  b_hash_to_list/2]).
+	 b_hash_to_list/2
+	]).
 
-:- use_module(library(lists), [
+:- use_module(library(lists),
-          delete/3,
+	[member/2]).
-	  nth0/3,
-	  member/2]).
 
 :- use_module(library(maplist)).
 
-:- use_module(library(pfl), [
+:- use_module(library(atts)).
-          factor/6,
+
+:- use_module(library(pfl),
+	[factor/6,
 	 defined_in_factor/2,
-	  skolem/2]).
+	 skolem/2
+	]).
 
-:- use_module(library(clpbn/aggregates), [
+:- use_module(library(clpbn/aggregates),
-          avg_factors/5]).
+	[avg_factors/5]).
 
-:- use_module(library(clpbn/dists), [
+:- use_module(library(clpbn/dists),
-          dist/4]).
+	[dist/4]).
 
 :- dynamic currently_defined/1, queue/1, f/4.
 
@@ -140,7 +134,8 @@ do_propagate(_K) :-
 
 add_factor(factor(Type, Id, Ks, _, _Phi, Constraints), NKs) :-
 %	writeln(+Ks),
-	( Ks = [K,Els], var(Els)
+	(
+		Ks = [K,Els], var(Els)
 	->
 		% aggregate factor
 		once(run(Constraints)),

packages/CLPBN/clpbn/horus_ground.yap

@@ -34,7 +34,7 @@
 :- use_module(library('clpbn/display'),
           [clpbn_bind_vals/3]).
 
-:- use_module(library(clpbn/numbers)).
+:- use_module(library('clpbn/numbers')).
 
 :- use_module(library(charsio),
           [term_to_atom/2]).

packages/CLPBN/clpbn/ve.yap

@@ -22,7 +22,7 @@
 		     run_ve_ground_solver/3,
 		     call_ve_ground_solver/6]).
 		     
-:- attribute size/1, all_diffs/1.
+:- use_module(library(atts)).
 
 :- use_module(library(ordsets),
 	[ord_union/3, 
@@ -73,6 +73,8 @@
 :- use_module(library('clpbn/aggregates'),
 	      [check_for_agg_vars/2]).
 	      
+:- attribute size/1, all_diffs/1.	      
+
 %
 % uses a bipartite graph where bigraph(Vs, NFs, Fs)
 % Vs=map variables to lists of factors

packages/CLPBN/learning/em.yap

@@ -4,24 +4,21 @@
 
 :- module(clpbn_em, [em/5]).
 
-:- use_module(library(lists),
-	      [append/3,
-	       delete/3]).
-
 :- reexport(library(clpbn),
-	      [
+	[clpbn_flag/2,
-	       clpbn_flag/2,
+	 clpbn_flag/3
-	       clpbn_flag/3]).
+	]).
 
 :- use_module(library(clpbn),
 	[clpbn_init_graph/1,
 	 clpbn_init_solver/4,
 	 clpbn_run_solver/3,
+	 clpbn_finalize_solver/1,	       
 	 pfl_init_solver/5,
 	 pfl_run_solver/3,
-	       clpbn_finalize_solver/1,
 	 conditional_probability/3,
-	       clpbn_flag/2]).
+	 clpbn_flag/2
+	]).
 
 :- use_module(library('clpbn/dists'),
 	[get_dist_domain_size/2,
@@ -29,42 +26,49 @@
 	 dist_new_table/2,
 	 get_dist_key/2,
 	 randomise_all_dists/0,
-	       uniformise_all_dists/0]).
+	 uniformise_all_dists/0
+	]).
 
-:- use_module(library(clpbn/ground_factors),
+:- use_module(library('clpbn/ground_factors'),
 	[generate_network/5,
-	      f/3]).
+	 f/3
+	]).
 	
-:- use_module(library(bhash), [
+:- use_module(library('clpbn/utils'),
-          b_hash_new/1,
+	[check_for_hidden_vars/3,
-          b_hash_lookup/3,
+	 sort_vars_by_key/3
-	  b_hash_insert/4]).
+	]).
 
 :- use_module(library('clpbn/learning/learn_utils'),
 	[run_all/1,
 	 clpbn_vars/2,
 	 normalise_counts/2,
 	 compute_likelihood/3,
-	       soften_sample/2]).
+	 soften_sample/2
+	]).
+	
+:- use_module(library(bhash),
+	[b_hash_new/1,
+	 b_hash_lookup/3,
+	 b_hash_insert/4
+	]).
+
+:- use_module(library(matrix),
+	[matrix_add/3,
+	 matrix_to_list/2
+	]).
 	
 :- use_module(library(lists),
 	[member/2]).
 	
-:- use_module(library(maplist)).
-
-:- use_module(library(matrix),
-	      [matrix_add/3,
-	       matrix_to_list/2]).
-
 :- use_module(library(rbtrees),
 	[rb_new/1,
 	 rb_insert/4,
-	       rb_lookup/3]).
+	 rb_lookup/3
+	]).
+
+:- use_module(library(maplist)).
 
-:- use_module(library('clpbn/utils'),
-	      [
-	       check_for_hidden_vars/3,
-	       sort_vars_by_key/3]).
 
 :- meta_predicate em(:,+,+,-,-), init_em(:,-).
 
@@ -101,9 +105,9 @@ init_em(Items, State) :-
 %	randomise_all_dists,
 	% set initial values for distributions
 	uniformise_all_dists,
-	setup_em_network(Items, Solver, State).
+	setup_em_network(Items, State).
 
-setup_em_network(Items, Solver, state( AllDists, AllDistInstances, MargKeys, SolverState)) :-
+setup_em_network(Items, state(AllDists, AllDistInstances, MargKeys, SolverState)) :-
 	clpbn:use_parfactors(on), !,
 	% get all variables to marginalise
 	run_examples(Items, Keys, Factors, EList),
@@ -111,7 +115,7 @@ setup_em_network(Items, Solver, state( AllDists, AllDistInstances, MargKeys, Sol
 	generate_dists(Factors, EList, AllDists, AllDistInstances, MargKeys),
 	% setup solver, if necessary
 	pfl_init_solver(MargKeys, Keys, Factors, EList, SolverState).
-setup_em_network(Items, Solver, state( AllDists, AllDistInstances, MargVars, SolverVars)) :-
+setup_em_network(Items, state(AllDists, AllDistInstances, MargVars, SolverState)) :-
 	% create the ground network
 	call_run_all(Items),
 	% get all variables to marginalise
@@ -121,7 +125,7 @@ setup_em_network(Items, Solver, state( AllDists, AllDistInstances, MargVars, Sol
 	% remove variables that do not have to do with this query.
 	different_dists(AllVars, AllDists, AllDistInstances, MargVars),
 	% setup solver by doing parameter independent work.
-	clpbn_init_solver(MargVars, AllVars, _, SolverVars).
+	clpbn_init_solver(MargVars, AllVars, _, SolverState).
 
 run_examples(user:Exs, Keys, Factors, EList) :-
     Exs = [_:_|_], !,

packages/CLPBN/pfl.yap

@@ -1,10 +1,10 @@
 %
-% This module defines PFL, the prolog factor language.
+% This module defines PFL, the Prolog Factor Language.
 %
 %
 
-:- module(pfl, [
+:- module(pfl,
-		op(550,yfx,@),
+	[op(550,yfx,@),
 	 op(550,yfx,::),
  	 op(1150,fx,bayes),
 	 op(1150,fx,markov),
@@ -24,7 +24,8 @@
 	 set_clpbn_flag/2 as set_pfl_flag,
 	 conditional_probability/3,
 	 pfl_init_solver/5,
-	 pfl_run_solver/3]).
+	 pfl_run_solver/3
+	]).
 
 :- reexport(library(clpbn/horus),
 	[set_solver/1]).
@@ -32,7 +33,6 @@
 :- reexport(library(clpbn/aggregates),
 	[avg_factors/5]).
 
-
 :- ( % if clp(bn) has done loading, we're top-level
 	predicate_property(set_pfl_flag(_,_), imported_from(clpbn))
    ->
@@ -44,11 +44,13 @@
 	true
    ).
 
+:- use_module(library(atts)).
 
 :- use_module(library(lists),
 	[nth0/3,
 	 append/3,
-	 member/2]).
+	 member/2
+	]).
 	 
 :- dynamic factor/6, skolem_in/2, skolem/2, preprocess/3, evidence/2, id/1.